Hello everyone,
I am following this page to process fMRI data: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...
I am able to run until step-3 but at step 4, I am not sure what should be directory to run this command. If I run the command in SUBJECTS_DIR directory, it runs for a second and creates a mean*.config file. But next step 5 requires *.config file to run, not the mean*.config
Just a quick background: I preprocessed all subjects structural data using recon-all and the processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder after preprocessing functional data (after running step-3) is also in SUBJECTS_DIR path.
Any help would be greatly appreciated.
MJ
Hello again,
Somehow I figured out the error I had related to *.config. Now I am able to run successfully all the 8 steps for 1 subject. I can see all the files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, sig.nii.gz etc. But when I try to display any of these files using FreeView (after overlaying over inflated surface), it doesn't display anything and gives me error "freadFloat: fread failed".
I would really appreciate any suggestions how can I display functional connectivity maps?
Thanks, MJ
On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja mj70481@gmail.com wrote:
Hello everyone,
I am following this page to process fMRI data:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...
I am able to run until step-3 but at step 4, I am not sure what should be directory to run this command. If I run the command in SUBJECTS_DIR directory, it runs for a second and creates a mean*.config file. But next step 5 requires *.config file to run, not the mean*.config
Just a quick background: I preprocessed all subjects structural data using recon-all and the processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder after preprocessing functional data (after running step-3) is also in SUBJECTS_DIR path.
Any help would be greatly appreciated.
MJ
Martin,
You need to provide more details for us to help you. What version of FreeSurfer? What exactly did you type in the command line as both your analysis and your call to freeview?
If I were to take a wild guess, I would say you have the wrong surface loaded. That tutorial does the analysis on the fsaverage inflated surface.
hth d
On Tue, Apr 26, 2016 at 4:07 PM, Martin Juneja mj70481@gmail.com wrote:
Hello again,
Somehow I figured out the error I had related to *.config. Now I am able to run successfully all the 8 steps for 1 subject. I can see all the files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, sig.nii.gz etc. But when I try to display any of these files using FreeView (after overlaying over inflated surface), it doesn't display anything and gives me error "freadFloat: fread failed".
I would really appreciate any suggestions how can I display functional connectivity maps?
Thanks, MJ
On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja mj70481@gmail.com wrote:
Hello everyone,
I am following this page to process fMRI data:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...
I am able to run until step-3 but at step 4, I am not sure what should be directory to run this command. If I run the command in SUBJECTS_DIR directory, it runs for a second and creates a mean*.config file. But next step 5 requires *.config file to run, not the mean*.config
Just a quick background: I preprocessed all subjects structural data using recon-all and the processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder after preprocessing functional data (after running step-3) is also in SUBJECTS_DIR path.
Any help would be greatly appreciated.
MJ
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The "freadFloat: fread failed" is a warning, not an error, and can be ignored.
The ces.nii.gz, cesvar.nii.gz, sig.nii.gz files are surface overlays stored in a "volume" format, so they have to be viewed on the surface. You can do with this with something like:
$> tksurferfv fsaverage lh inflated -ov sig.nii.gz -fminmax 2 3
-Zeke
On 04/26/2016 04:07 PM, Martin Juneja wrote:
Hello again,
Somehow I figured out the error I had related to *.config. Now I am able to run successfully all the 8 steps for 1 subject. I can see all the files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, sig.nii.gz etc. But when I try to display any of these files using FreeView (after overlaying over inflated surface), it doesn't display anything and gives me error "freadFloat: fread failed".
I would really appreciate any suggestions how can I display functional connectivity maps?
Thanks, MJ
On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja <mj70481@gmail.com mailto:mj70481@gmail.com> wrote:
Hello everyone, I am following this page to process fMRI data: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough I am able to run until step-3 but at step 4, I am not sure what should be directory to run this command. If I run the command in SUBJECTS_DIR directory, it runs for a second and creates a mean*.config file. But next step 5 requires *.config file to run, not the mean*.config Just a quick background: I preprocessed all subjects structural data using recon-all and the processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder after preprocessing functional data (after running step-3) is also in SUBJECTS_DIR path. Any help would be greatly appreciated. MJ
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Zeke,
Thank you so much ! It's working really well now. I have one more question- is there any way I can display labels (name of the areas) as well on the maps I see (using tksurfer command you suggested).
Thanks Zeke once again.
On Tue, Apr 26, 2016 at 4:44 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
The "freadFloat: fread failed" is a warning, not an error, and can be ignored.
The ces.nii.gz, cesvar.nii.gz, sig.nii.gz files are surface overlays stored in a "volume" format, so they have to be viewed on the surface. You can do with this with something like:
$> tksurferfv fsaverage lh inflated -ov sig.nii.gz -fminmax 2 3
-Zeke
On 04/26/2016 04:07 PM, Martin Juneja wrote:
Hello again,
Somehow I figured out the error I had related to *.config. Now I am able to run successfully all the 8 steps for 1 subject. I can see all the files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, sig.nii.gz etc. But when I try to display any of these files using FreeView (after overlaying over inflated surface), it doesn't display anything and gives me error "freadFloat: fread failed".
I would really appreciate any suggestions how can I display functional connectivity maps?
Thanks, MJ
On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja <mj70481@gmail.com mailto:mj70481@gmail.com> wrote:
Hello everyone, I am following this page to process fMRI data:http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...
I am able to run until step-3 but at step 4, I am not sure what should be directory to run this command. If I run the command in SUBJECTS_DIR directory, it runs for a second and creates a mean*.config file. But next step 5 requires *.config file to run, not the mean*.config Just a quick background: I preprocessed all subjects structural data using recon-all and the processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder after preprocessing functional data (after running step-3) is also in SUBJECTS_DIR path. Any help would be greatly appreciated. MJ
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I dont see an obvious way but I dont use this tool often. You may want to create a new post and ask others.
-Zeke
On 04/26/2016 06:01 PM, Martin Juneja wrote:
Hi Zeke,
Thank you so much ! It's working really well now. I have one more question- is there any way I can display labels (name of the areas) as well on the maps I see (using tksurfer command you suggested).
Thanks Zeke once again.
On Tue, Apr 26, 2016 at 4:44 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
The "freadFloat: fread failed" is a warning, not an error, and can be ignored. The ces.nii.gz, cesvar.nii.gz, sig.nii.gz files are surface overlays stored in a "volume" format, so they have to be viewed on the surface. You can do with this with something like: $> tksurferfv fsaverage lh inflated -ov sig.nii.gz -fminmax 2 3 -Zeke On 04/26/2016 04:07 PM, Martin Juneja wrote: > Hello again, > > Somehow I figured out the error I had related to *.config. Now I am able > to run successfully all the 8 steps for 1 subject. I can see all the > files generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, > sig.nii.gz etc. > But when I try to display any of these files using FreeView (after > overlaying over inflated surface), it doesn't display anything and gives > me error "freadFloat: fread failed". > > I would really appreciate any suggestions how can I display functional > connectivity maps? > > Thanks, > MJ > > On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja <mj70481@gmail.com <mailto:mj70481@gmail.com> > <mailto:mj70481@gmail.com <mailto:mj70481@gmail.com>>> wrote: > > Hello everyone, > > I am following this page to process fMRI data: >http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough > > I am able to run until step-3 but at step 4, I am not sure what > should be directory to run this command. If I run the command in > SUBJECTS_DIR directory, it runs for a second and creates a > mean*.config file. But next step 5 requires *.config file to run, > not the mean*.config > > Just a quick background: > I preprocessed all subjects structural data using recon-all and the > processed folders are in my FreeSurfer SUBJECTS_DIR path and the > folder after preprocessing functional data (after running step-3) is > also in SUBJECTS_DIR path. > > Any help would be greatly appreciated. > > MJ > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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